Check out the powered subs at Soundtrack or Circuit City. There are a few out there that will fit under the seat pointing up, and they really do sound impressive. I listened to an Infinity and I really fell in love with that one.
Another idea is, move the gas tank to a safer location than under your butt, and then any number of standard sub boxes would probably fit where the gas tank sits.
The nice thing about subwoofers is that bass will travel through anything, so it really doesn't matter where you put it. It's the treble you have to be careful with.
Where are you going to put your other speakers, out of curiosity?
I was thinking of putting a pair of tweeters up in the headliner, and midrange speakers in pine boxes kind of on the firewall under the dash. Then a powered sub under the seat.
